R.E.DD.B.: code F-29

Upload 11-01-2006 10:45 (Day-Month-Year, Paris time)
Update 28-09-2011 13:01 (Day-Month-Year, Paris time)

Information about the Author (who submitted the project in R.E.DD.B.)

Firstname Francois-Yves

Lastname Dupradeau

Institute UFR de pharmacie, UPJV

City Amiens

Country FRANCE

General information about the Project

Molecule keywords

NTYM

C10H13O2N

(+)NH3-terminal fragment of O-methyl-L-tyrosine

Ammonium

Peptide bond

Abstract

RESP atomic charges for the (+)NH3-terminal fragment of O-methyl-L-tyrosine, (+)NH3CHCH2PhOMeCO, (charges derived using Methylammonium and N-Acetyl-O-methyl-L-tyrosine-N'-methylamide; conformations: phi = -72.41, psi = -34.82, chi = -171.96 and phi = -119.15, psi = 138.71, chi = -60.94) based on the Connolly surface algorithm and the HF/6-31G* theory level. Charges suitable for MD simulations using the Cornell et al. AMBER force field (and/or its adaptations). Charges derived using 2 mol. orientations (rigid-body reorientation algorithm, RBRA implemented in the R.E.D. program) for MeNH3(+), and 2 mol. conformations and 4 mol. orientations (RBRA) for each conformation for ACE-TYM-NME. Charge values to be compared with those reported in the projects F-30, F-31 and F-32. For information about O-methyl-L-tyrosine, see P. Schultz's laboratory.

Publication YES

Author(s) F.-Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski and P. Cieplak

Journal Phys. Chem. Chem. Phys.

Year 2010

Volume 12

Page(s) 7821-7839

"Whole molecule" or "Molecule fragment" type project MOLECULE FRAGMENT

Interface R.E.D. used ? YES

Charge derivation procedure

Number of Tripos mol2 file(s) provided by the author(s) 1

Contain charge values & information about molecular topology

No	Name	Download	Wikipedia	3D Display 1	3D Display 2
1	N-terminal charged fragment of O-methyl-L-tyrosine

Number of molecule(s) used in the charge derivation procedure 2

File(s) provided to the PDB format

No	Molecule name	Conformation No	Reorientation procedure	Mol. orientation No	Download	Wikipedia
1	Methylammonium	1	Rigid Body Reorient Algo	2
2	N-Acetyl-O-methyl-L-tyrosine-N'-methylamide	2	Rigid Body Reorient Algo	4

Information regarding Quantum Calculations

Geometry optimization

Program 1 GAUSSIAN 1998

Theory level 1 HF

More information 1 Opt=VTight

Basis set 1 6-31G*

Molecular electrostatic potential computation

Program 2 GAUSSIAN 1998

Theory level 2 HF

More information 2 IOp(6/33=2) NoSymm

Basis set 2 6-31G*

Algorithm CONNOLLY SURFACE

Information about the charge fit

Program RESP

Number of stage(s) 2

input of stage 1

input of stage 2

Files the author of the project wishes to provide...

A script to convert Tripos mol2 file(s) into LEaP OFF library(ies) (for AMBER)...

A script to convert Tripos mol2 file(s) into RTF or PSF library(ies) (for CHARMM)...

A file to provide new force field parameters compatible with the Tripos mol2 file(s)...

A file (choice made by the author) to provide more information about the project...

Download the whole project...